Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.47
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.966 kcal/mol/HA)
✓ Good fit quality (FQ -8.53)
✓ Good H-bonds (5 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Very high strain energy (34.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-22.224
kcal/mol
LE
-0.966
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.24
cLogP
Interaction summary
HB 5
HY 23
PI 3
CLASH 2
Interaction summary
HB 5
HY 23
PI 3
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.706 | Score | -22.224 |
|---|---|---|---|
| Inter norm | -0.953 | Intra norm | -0.013 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; high strain Δ 34.5 | ||
| Residues |
GLU18
GLY13
GLY49
ILE106
ILE339
LEU17
MET113
SER109
SER14
TRP21
TYR110
VAL53
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 8 | Native recall | 0.62 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 298 | 0.38144530618098743 | -1.36746 | -29.7402 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 332 | 1.5323581236557415 | -0.965372 | -23.4942 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 269 | 1.5509765435606315 | -1.15851 | -26.1501 | 10 | 14 | 0 | 0.00 | - | - | no | Open |
| 309 | 1.7055009856603602 | -0.952849 | -22.2241 | 5 | 12 | 8 | 0.62 | - | - | no | Current |
| 333 | 2.079196184252758 | -0.874451 | -20.6877 | 9 | 11 | 0 | 0.00 | - | - | no | Open |
| 345 | 2.5813274272129556 | -1.18482 | -28.0426 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 292 | 2.624262509121678 | -1.04406 | -21.6326 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 360 | 2.9336237751662444 | -1.13823 | -28.8935 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 243 | 4.071980294350336 | -1.08338 | -23.8695 | 13 | 13 | 0 | 0.00 | - | - | no | Open |
| 255 | 4.429079194341519 | -1.2511 | -28.5426 | 10 | 13 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.224kcal/mol
Ligand efficiency (LE)
-0.9663kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.528
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-21.97kcal/mol
Minimised FF energy
-56.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
557.7Ų
Total solvent-accessible surface area of free ligand
BSA total
421.3Ų
Buried surface area upon binding
BSA apolar
271.4Ų
Hydrophobic contacts buried
BSA polar
149.9Ų
Polar contacts buried
Fraction buried
75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2995.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1452.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)